Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011625.1 Kokia drynarioides strain JFW-HI SEQ_126616, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 3625
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2435 original size:60 final size:60

Alignment explanation


    Indices: 2360--2549  Score: 299
    Period size: 60  Copynumber: 3.1  Consensus size: 60

       2350 TCTAATAATT

                *     *     *                                           
       2360 AAATAATGATCCACGTAATAATAATTTAGCTTTTCAATTTGATAAATAATTTTTTAGTGA
          1 AAATGATGATACACGTGATAATAATTTAGCTTTTCAATTTGATAAATAATTTTTTAGTGA

                                                             *   *  *   
       2420 AAATGATGATACACGTGATAATAATTTAGCTTTTCAATTTGATAAATAAATTTCTAATGA
          1 AAATGATGATACACGTGATAATAATTTAGCTTTTCAATTTGATAAATAATTTTTTAGTGA

                                   *                        *            
       2480 AAATGATGATACACGTGATAATATTTTAGCTTTTCAATTTGATAAATAGTTATTTTAGTGA
          1 AAATGATGATACACGTGATAATAATTTAGCTTTTCAATTTGATAAATAATT-TTTTAGTGA

                     
       2541 AAATGATGA
          1 AAATGATGA

       2550 GGTGTTTCAT


Statistics
Matches: 118,  Mismatches: 11, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  60  102  0.86
  61   16  0.14

ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40


Consensus pattern (60 bp):   
AAATGATGATACACGTGATAATAATTTAGCTTTTCAATTTGATAAATAATTTTTTAGTGA

Found at i:2793 original size:24 final size:24

Alignment explanation


    Indices: 2730--2800  Score: 74
    Period size: 22  Copynumber: 3.0  Consensus size: 24

       2720 AAAATTAAAT

                         *  **      
       2730 TTTATATTTTTATGATAGTAAAA-
          1 TTTATATTTTTATAATTTTAAAAG

                  *      *          
       2753 -TTATAATTTTATTATTTTAAAAG
          1 TTTATATTTTTATAATTTTAAAAG

                                     
       2776 TTTATATTTTTATAATTTTTAAAAG
          1 TTTATATTTTTATAA-TTTTAAAAG

       2801 ATTAAATTAA


Statistics
Matches: 39,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  22   18  0.46
  24   12  0.31
  25    9  0.23

ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56


Consensus pattern (24 bp):   
TTTATATTTTTATAATTTTAAAAG
Done.